Efficient solution of nonlinear ordinary differential equations expressed in S-system canonical form
SIAM Journal on Numerical Analysis
Handbook of theoretical computer science (vol. B)
The algorithmic analysis of hybrid systems
Theoretical Computer Science - Special issue on hybrid systems
Measuring the performance of communication middleware on high-speed networks
Conference proceedings on Applications, technologies, architectures, and protocols for computer communications
Proving properties of continuous systems: qualitative simulation and temporal logic
Artificial Intelligence
On Group Communication Support in CORBA
IEEE Transactions on Parallel and Distributed Systems
Improving the Performance of Distributed CORBA Applications
IPDPS '02 Proceedings of the 16th International Parallel and Distributed Processing Symposium
Design and Implementation of a Pluggable Fault Tolerant CORBA Infrastructure
IPDPS '02 Proceedings of the 16th International Parallel and Distributed Processing Symposium
Hybrid Modeling and Simulation of Biomolecular Networks
HSCC '01 Proceedings of the 4th International Workshop on Hybrid Systems: Computation and Control
Qualitative simulation of genetic regulatory networks: method and application
IJCAI'01 Proceedings of the 17th international joint conference on Artificial intelligence - Volume 1
Modeling Cellular Behavior with Hybrid Automata: Bisimulation and Collapsing
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
Taming the complexity of biochemical models through bisimulation and collapsing: theory and practice
Theoretical Computer Science - Special issue: Computational systems biology
Approximation of dynamical systems using s-systems theory: application to biological systems
Proceedings of the 2005 international symposium on Symbolic and algebraic computation
Probabilistic Approximations of Signaling Pathway Dynamics
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Algebraic systems biology: theses and hypotheses
AB'07 Proceedings of the 2nd international conference on Algebraic biology
Probabilistic approximations of ODEs based bio-pathway dynamics
Theoretical Computer Science
An agent-oriented conceptual framework for systems biology
Transactions on Computational Systems Biology III
| Hi-index | 0.00 |
Several biological and biochemical mechanisms can be modeled with relatively simple sets of differential algebraic equations (DAE). The numerical solution to these differential equations provide the main investigative tool for biologists and biochemists. However, the set of numerical traces of very complex systems become unwieldy to wade through when several variables are involved. To address this problem, we propose a novel way to query large sets of numerical traces by combining in a new way well known tools from numerical analysis, temporal logic and verification, and visualization.In this paper we describe XS-systems: computational models whose aim is to provide the users of S-systems with the extra tool of an automaton modeling the temporal evolution of complex biochemical reactions. The automaton construction is described starting from both numerical and analytic solutions of the differential equations involved, and parameter determination and tuning are also considered. A temporal logic language for expressing and verifying properties of XS-systems is introduced and a prototype implementation is presented.